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Journal of Bioinformatics and Computational Biology

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https://www.readbyqxmd.com/read/28403667/a-computational-model-for-predicting-transmembrane-regions-of-retroviruses
#1
Ze Liu, Hongqiang Lv, Jiuqiang Han, Ruiling Liu
Transmembrane region (TR) is a conserved region of transmembrane (TM) subunit in envelope (env) glycoprotein of retrovirus. Evidences have shown that TR is responsible for anchoring the env glycoprotein on the lipid bilayer and substitution of the TR for a covalently linked lipid anchor abrogates fusion. However, universal software could not achieve sufficient accuracy as TM in env also has several motifs such as signal peptide, fusion peptide and immunosuppressive domain composed largely of hydrophobic residues...
March 21, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28317416/editorial-bioinformatics-development-at-the-bgrs-sb-conference-series-10th-anniversary
#2
Yuriy L Orlov, Nikolay A Kolchanov, Ralf Hofestädt, Limsoon Wong
No abstract text is available yet for this article.
March 20, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28403668/neat-flex-predicting-the-conformational-flexibility-of-amino-acids-using-neuroevolution-of-augmenting-topologies
#3
Bruno Grisci, Márcio Dorn
The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT-FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally...
March 16, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28351215/quantitative-analysis-of-the-heterogeneous-population-of-endocytic-vesicles
#4
Konstantin Kozlov, Vera Kosheverova, Rimma Kamentseva, Marianna Kharchenko, Alena Sokolkova, Elena Kornilova, Maria Samsonova
The quantitative characterization of endocytic vesicles in images acquired with microscope is critically important for deciphering of endocytosis mechanisms. Image segmentation is the most important step of quantitative image analysis. In spite of availability of many segmentation methods, the accurate segmentation is challenging when the images are heterogeneous with respect to object shapes and signal intensities what is typical for images of endocytic vesicles. We present a Morphological reconstruction and Contrast mapping segmentation method (MrComas) for the segmentation of the endocytic vesicle population that copes with the heterogeneity in their shape and intensity...
March 7, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28345370/an-accurate-and-fast-alignment-free-method-for-profiling-microbial-communities
#5
Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan
Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Although homology-based methods are popular, they have shown to be computationally expensive due to the alignment of tens of millions of reads from metagenomic samples to reference genomes of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers (GSM)...
March 7, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28335678/computational-study-on-transfer-of-l-ascorbic-acid-by-ulaa-through-escherichia-coli-membrane
#6
Ehsan Faghih-Mirzaee, Maryam Dehestani, Leila Zeidabadinejad
In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli (E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6[Formula: see text]311[Formula: see text]G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated...
February 24, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28274175/the-origins-and-evolutionary-history-of-human-non-coding-rna-regulatory-networks
#7
Masih Sherafatian, Seyed Javad Mowla
The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human...
February 1, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28052708/chaos-and-hyperchaos-in-simple-gene-network-with-negative-feedback-and-time-delays
#8
Tamara M Khlebodarova, Vladislav V Kogai, Stanislav I Fadeev, Vitaly A Likhoshvai
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28033735/pass-based-approach-to-predict-hiv-1-reverse-transcriptase-resistance
#9
Olga Tarasova, Dmitry Filimonov, Vladimir Poroikov
HIV reverse transcriptase (RT) inhibitors targeting the early stages of virus-host interactions are of great interest to scientists. Acquired HIV RT resistance happens due to mutations in a particular region of the pol gene encoding the HIV RT amino acid sequence. We propose an application of the previously developed PASS algorithm for prediction of amino acid substitutions potentially involved in the resistance of HIV-1 based on open data. In our work, we used more than 3200 HIV-1 RT variants from the publicly available Stanford HIV RT and protease sequence database already tested for 10 anti-HIV drugs including both nucleoside and non-nucleoside RT inhibitors...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27908222/contribution-of-bacterial-promoter-elements-to-transcription-start-site-detection-accuracy
#10
Milos Nikolic, Tamara Stankovic, Marko Djordjevic
Accurately detecting transcription start sites (TSS) is a starting point for understanding gene transcription, and an important ingredient in a number of applications necessary for functional gene annotation, such as gene and operon predictions. Available methods for TSS detection in bacteria use very different description of the bacterial promoter structure and all of them show low accuracy. It is therefore unclear which promoter features should be included in TSS recognition, and how their accuracy impacts the search detection...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27832721/identification-of-residues-of-the-archaeal-rna-binding-nip7-proteins-specific-to-environmental-conditions
#11
Kirill E Medvedev, Nikolay A Kolchanov, Dmitry A Afonnikov
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism's habitat. The number of such positions related to pressure change is much lower than related to temperature change...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28238281/new-multilocus-linkage-disequilibrium-measure-for-tag-snp-selection
#12
Bo Liao, Xiangjun Wang, Wen Zhu, Xiong Li, Lijun Cai, Haowen Chen
Numerous approaches have been proposed for selecting an optimal tag single-nucleotide polymorphism (SNP) set. Most of these approaches are based on linkage disequilibrium (LD). Classical LD measures, such as D' and r(2), are frequently used to quantify the relationship between two marker (pairwise) linkage disequilibria. Despite of their successful use in many applications, these measures cannot be used to measure the LD between multiple-marker. These LD measures need information about the frequencies of alleles collected from haplotype dataset...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28201946/sorting-permutations-by-prefix-and-suffix-rearrangements
#13
Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias
Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178889/v-elmpirnapred-identification-of-human-pirnas-by-the-voting-based-extreme-learning-machine-v-elm-with-a-new-hybrid-feature
#14
Cong Pian, Yuan-Yuan Chen, Jin Zhang, Zhi Chen, Guang-Le Zhang, Qiang Li, Tao Yang, Liang-Yun Zhang
Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this paper, we introduce a series of new features with 80 dimension called short sequence motifs (SSM). A hybrid feature vector with 1444 dimension can be formed by combining 1364 features of [Formula: see text]-mer strings and 80 features of SSM features. We optimize the 1444 dimension features using the feature score criterion (FSC) and list them in descending order according to the scores...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178888/histone-modifications-influence-skipped-exons-inclusion
#15
Yue Hou, Huan Huang, Wenqiao Hu, Hongde Liu, Xiao Sun
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28150521/drug-repurposing-and-therapeutic-anti-microrna-predictions-for-inhibition-of-oxidized-low-density-lipoprotein-induced-vascular-smooth-muscle-cell-associated-diseases
#16
Shun-Tsung Chen, Chien-Hung Huang, Victor C Kok, Chi-Ying F Huang, Jin-Shuei Ciou, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng
Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27989220/mathematical-model-of-lsrr-binding-and-derepression-in-escherichia-coli-k12
#17
Steven M Graff, William E Bentley
Quorum sensing (QS) enables bacterial communication and collective behavior in response to self-secreted signaling molecules. Unlocking its genetic regulation will provide insight towards understanding its influence on pathogenesis, formation of biofilms, and many other phenotypes. There are few datasets available that link QS-mediated gene expression to its regulatory components and even fewer mathematical models that incorporate known mechanistic detail. By integrating these data with annotated sequence information, mathematical inferences can be pieced together that shed light on regulatory structure...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27899048/the-method-for-breast-cancer-grade-prediction-and-pathway-analysis-based-on-improved-multiple-kernel-learning
#18
Tianci Song, Yan Wang, Wei Du, Sha Cao, Yuan Tian, Yanchun Liang
Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer grade can markedly elevate the detection of early breast cancer and efficiently guide its treatment. With the advent of high-throughput profiling technology, a large number of data of different types are rapidly generated, and each data provides its unique biological insight...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27411307/a-machine-learning-approach-for-predicting-palmitoylation-sites-from-integrated-sequence-based-features
#19
Liqi Li, Qifa Luo, Weidong Xiao, Jinhui Li, Shiwen Zhou, Yongsheng Li, Xiaoqi Zheng, Hua Yang
Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27397631/an-improved-method-for-predicting-interactions-between-virus-and-human-proteins
#20
Byungmin Kim, Saud Alguwaizani, Xiang Zhou, De-Shuang Huang, Byunkyu Park, Kyungsook Han
The interaction of virus proteins with host proteins plays a key role in viral infection and consequent pathogenesis. Many computational methods have been proposed to predict protein-protein interactions (PPIs), but most of the computational methods are intended for PPIs within a species rather than PPIs across different species such as virus-host PPIs. We developed a method that represents key features of virus and human proteins of variable length into a feature vector of fixed length. The key features include the relative frequency of amino acid triplets (RFAT), the frequency difference of amino acid triplets (FDAT) between virus and host proteins, and amino acid composition (AC)...
February 2017: Journal of Bioinformatics and Computational Biology
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